I think a lot of you missed the part where this quest line continues in 5.1, 5.2, and 5.3. There are 3 more parts confirmed for later patches, so I'm guessing this gem isn't the end-all-be-all legendary. I think this is the first step in a quest line to an actual legendary. My theory (no evidence on this at all) is that ultimately those weapons will become BiS through legendary upgrades across the patches until they actually become individual legendary weapons, with all the cool procs that go along with that. Or at least I hope. Also, I agree that LFR content shouldn't be dropping parts of the legendary quest. Legendary items are supposed to represent work, dedication, a ton of luck, and skill (I'm not saying that they have lately, seeing the rogue daggers and staff on every other player in arenas), and I think AFKing out for a few minutes then getting part of a legendary is going against this philosophy. I would be fine, however, if just this part and the next part even are available to LFR and then the final one or two quests required normal/heroic, that way casuals can get their nice semi-legendaries and hardcores that want to spend hours farming for it can do that as well for a slightly better version.

Considering the LFR versions of the weapons have the Sha slot, maybe it's intended to be able to do the questline in LFR. If it rewards a weaker version of the crystal by doing it via LFR, I see no problem with it. And since it looks like Wrathion's questline is going to be one of the major plotlines for Pandaria, it'd be nice to see it as well via LFR.

I'd be fine with this coming from LFR as long as you can get the gem back out if you progress into Normals and Heroics and get a better version of the weapon. If you only can do it once and get the gem once...

What about agi gems?
Also what if one put this gem into a weapon. He then get a upgrade. can he take the gem out and put it in a new one? Or can he buy a new one? or is it stuck forever and sucks to be you then?

5.1: Have a drink with Wrathion. Get a Sha-Touched epic weapon in your raid.
5.2: Get some marks that resemble the Triforce (you supply your courage for the other two). He makes you a gem that resonates with that sha-touched weapon
5.3: In return for 1,000 (insert grindy thingy here], he gives you his breath, which purifies the Sha-Touched weapon, turning it into a legendary Purified Weapon.

What about agi gems?
Also what if one put this gem into a weapon. He then get a upgrade. can he take the gem out and put it in a new one? Or can he buy a new one? or is it stuck forever and sucks to be you then?

Yeah we really need to know if you can either repeat the questline to get more gems, or get new ones some other way. Especially if we can use them in weapons from the next tiers. Its possible we will be upgrading the weapons with each tier which for me would not be cool since I play hunter, dont like guns, and it has mastery. Thank god for transmog.